Exam 3 Flashcards
Chapters 15-17 (82 cards)
1
Q
Amino Acids
A
- Repeating unit of proteins
- Consists of amino group, carboxyl group, hydrogen atom, and variable R group
2
Q
Peptide Bonds
A
-Chemical bond that connects amino acids in a protein
3
Q
Polypeptide Chain
A
- Chain of amino acids linked by peptide bonds
- Protein
4
Q
One gene, one polypeptide hypothesis
A
-Each gene encodes a separate polypeptide chain
5
Q
Sense Codons
A
-Codon that specifies an amino acid in a protein
6
Q
Degenerate
A
-Refers to the fact that the genetic code contains more codons than are needed to specify all 20 AAs
7
Q
Synonymous Codons
A
-Diff codons that specify the same codon
8
Q
Isoaccepting tRNAs
A
-Diff tRNAs w/ diff anticodons that spcify the same AA
9
Q
Nonoverlapping
A
-Each nucleotide is a part of only 1 codon and encodes only 1 AA in a protein
10
Q
Reading frame
A
- Particular way in which a nucleotide sequence is read in groups of 3 nucs (codon) in translation
- Begins w start codon and ends w/ stop codon
11
Q
Initiation/ start codon
A
- Codon that specifies the 1st AA of protein
- fMet in prok, Met in Euk
- Most commonly AUG
12
Q
Stop/Termination/Nonsense codons
A
- Codon in mRNA that signals the end of translation
- UAA, UAG, UGA
13
Q
Aminoacyl-tRNA sythetases
A
- Enzyme that attaches an amino acid to tRNA
- Specific for a particular AA
14
Q
tRNA charging
A
-Chemical rxn in which an aminoacyl-tRNA sythetase attaches an AA to its corresponding tRNA
15
Q
IF3
A
- Protein required for the initiation of translation in proks
- Binds to the small subunit of the ribosome and prevents the large subunit from binding during initiation
16
Q
IF1
A
- Protein required for initiation of translation in proks
- Enhances disociation of the large and small subunits of the ribosome
17
Q
IF2
A
- Protein required for initiation of translation in proks
- Forms a complex w/ GTP and charged tRNA & delivers charged tRNA to initiator complex
18
Q
30s initiator complex
A
- Initial complex formed in the initiation of translayion in proks
- Consists of small subunit of ribosome, mRNA, initiator tRNA charged w fMet, GTP, and IFs 1,2, and 3
19
Q
70s initiator complex
A
- Final complex formed in the initiation of translation in proks
- Small and large ribosomal subunits, mRNA, and intiator tRNA charged w fMet
20
Q
Cap binding complex
A
- A group of proteins in euks
- Binds to 5’ cap and initiates translation
- Aids in exporting mRNA from nucleus to cytoplasm
- Promotes initial/pioneer round of translation
21
Q
Aminoacyl (A) site
A
- One of 3 sites in a ribosome occupied by a tRNA during translation
- All charged tRNAs w/ expection of initiator tRNAs first enter the A site
22
Q
Peptidyl (P) site
A
- One of 3 sites in a ribosome occupied by a tRNA during translation
- In elongation stage, tRNAs move from A to P site
23
Q
Exit (E) site
A
- One of 3 sites in a ribosome occupied by a tRNA during translation
- In elongation stage, tRNA moves from P to E site
- –Exits the ribosome
24
Q
Elongation Factor Tu (EF-Tu)
A
- Protein taking part in the elongation stage of translation
- Forms a complex w/ GTP and charged tRNA
- Delivers charged tRNA to ribosome
25
Elongation Factor Ts (EF-Ts)
-Protein that regenerates EF-Tu in elongation stage of translation
26
Translocation
-Movement of a ribosome along mRNA in the course of translation
27
Elongation Factor G
- EF-G
| - Protein that combines w/ GTP and is required for movement of the ribosome along the mRNA during translation
28
Release Factors
- Protein required for termination of translation
- Binds to ribosome when a stop codon is reached and stimulates the release of the polypeptide chain, the tRNA, and the mRNA from the ribsome
- Euk cell requires eRF-1 and eRF-2
- Proks require RF-1, RF-2, and RF-3
29
Structural Genes
-DNA sequence that encodes a protein that fxns in metabolism or biosynthesis or that has a structural role in the cell
30
Constitutive
-A gene that is expressed continually w/o regulation
31
Regulatory elements
-DNA sequence that affects the transcription of other DNA sequences to which it is physically linked
32
Domian
-Functional part of protein
33
Operon
-Set of structural genes in a prok. cell, along with their common promoter and other sequences (operator) that control their transcription
34
Regulator Gene
- Gene associated w an operon in prok cells
| - Encode a protein or RNA molecule that fxns in controlling the transcription of one or more structural genes
35
Regulator Protein
- Protein produced by a regulator gene
| - Binds to another DNA sequence (operator) and controls the transcription of one or more structural genes
36
Operator
- DNA sequence in an operon of prok cells
- A regulator protein beings to
- Binding affects rate of transcription of structural genes
37
Neg control
- Gene reg in which the binding of a regulator protein to DNA inhibits transcription
- Reg protein= repressor
38
Positive control
- Gene reguation in which binding of a reg protein to DNA stimulates transcription
- reg protein= activator
39
Inducible operons
-Operon in which transcription is normally turned off so that something must occur for transcription to be induced/turned on
40
Repressible Operons
-Operon in which transcription is normally turned on, so that something must happen for transcriotion to be repressed/turned off
41
Inducer
- Substance that stimulates transcription in an inducible system of gene regulations
- Usually a molecule that binds to a repressor protein, alters that repressor so that it cannot bind to DNA and inhibit transcription
42
Allosteric Proteins
-Protein that changes confirmation upon binding w another molecule
43
Corepressor
- Substance that inhibits transcription in a repressible system of gene regulation
- Molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription
44
Coordinate Induction
-The simultaneous synthesis of several enzymes stimulated by a single environmental factor
45
Partial Diploid
- Prok cells that possess 2 copies of the same genes
| - -One on chromosome, one on plasmid
46
Catabolite Repression
- System of gene control in prok. operons
| - Glucose is used preferentially and the metabolism of other sugas is repressed in the presence of glucose
47
Catabolite Activator Protein (CAP)
- Proteins that fxn in catabolite repression
| - When bound w cAMP, CAP binds to the promoter of certain operons and stimulates transcription
48
cAMP
- Modified nucleotide that fxns in catabolite repression
- Low levels of glucose stimulate high levels of cAMP
- --cAMP attaches to CAP, which binds to the promoters of certain operons and stimulates transcription
49
Attenuation
- Type of gene regulation in some prok operons
| - Transcription is initiated but terminates prematurely b4 transcription of structural genes
50
Attenuator
- Secondary structure that forms in the 5' untranslated region of some operons
- Causes the premature termination of transcription
51
Antiterminator
-Protein or DNA sequence that inhibits the termination of transcription
52
Antisense RNA
- Small RNA mol that bps w a complementary DNA or RNA sequence and affects its fxning
- Control gene expression by binding to sequences on mRNA and inhibiting its translation
53
Riboswitches
- Regulatory sequence in an RNA molecule
- When inducer binds to riboswitch, binding changes the configuration of the RNA molecule and alters the expression of RNA
- -Usually by affecting the termination of transcription or translation
54
Structural Genes on the Lac Operon
- Lac Z--> gene that makes B galactosidase enzyme
- Lac Y--> Permease
- --Allows lactose into cell
- Lac A--> Transacetylase
55
Lac I
-Regulator gene, encode regulator protein
-Lac I- = nonfunctional repressor protein
-Lac I^s= superrepressor, allolactose cannot bind to it
-Trans
Lac I s> Lac I+ > Lac I-
56
Lac O
-operator
-Cis
-LacO^C= Repressor cannot bind to operator region
Lac O c> Lac O+
*Can transcribe structural genes w or w/o lactose
57
Lac Operon
- Ex of negative inducible operon
- When lactose levels= high, allolactose converted to lactose by B-galactose, binds to repressor protein
- --Repressor cannot bind to operator, transcription occurs
- Lactose levels= low, no allolactose, transcription is inhibited
- --Repressor can bind to operator
58
DNase I hypersensitivity sites
-Chromatin region that becomes sensitive to digestion by enzyme DNase I
59
Chomatin remodeling complexes
-Complex of proteins that alters chromatin structure w/o acetylating histone proteins
60
Histone code
- Modifications in histone proteins
| - Add. or removal of phosphate, methyl, or acetyl groups that encode info affecting how genes are expressed
61
CpG islands
- DNA region that contains many copies of a cytosine base followed by a guanine base
- Often found near transcription start sites in euk DNA
- Cytosine base in CpG commonly methylated when genes are inactive
- --Demethylated b4 initiation of transcription
- METHYLATED DNA=REPRESSED TRANSCRIPTION
62
3 processes that affect gene regulation by altering chromatin structure
- Chromatin remodeling
- Modification of histone proteins
- DNA methylation
63
Methylation of histones
- Histone methyltransferases= add CH3 to histones
- Histone Demethylases= remove CH3
- Activates or represses transcription
64
Acetylation of Histones
- Addition stimulates transcription
- CH3CO
- Add by acetyltransferase
- Removed by deacetylases (represses transcription)
65
Arabidopsis and Flowering
- FLD stimulates flowering by deacetylating chromatin around FLC
- FLC inhibits flowering, when acetyl groups removed it is inhibited
66
Mediators
-Complex of proteins that is one of the components of the basal transcription apparatus
67
Insulators
- DNA sequences that blocks or insulates the effect of an enhancer
- Must be located btwn promoter and enhancer to block activity
- May also limit the spread of changes in chromatin structure
68
Response Elements
- DNA sequence shared by promoters or enhancers of several euk genes
- Regulatory proteins can bind to stimulate the coordinate transcription of these genes
69
Regulation of Galactose Metabolism Through Gal4
- Gal4= transcriptional activator protein
- galactose low= genes not transcribed
- --High= genes r transcribed and galactose broken down
- Gal4 binds to UASg--> activates transcription needed to metabolize galactose
- Gal4 and Gal80 bind--> prevents transcription when gal=low
- When galactose= present, Gal3 binds to Gal80 so it cant bind to Gal4--> transcription occurs and galactose is metabolized
70
siRNAs scilence transcription by altering chromatin structure
- siRNA combines w protein to create RITS
- Binds to complementary sequence in DNA or RNA molecule in process of being transcribed, repressing transcription by attracting enzymes that methylate histones
71
Bacterial Enhancers
- Element that affects transcription but far from gene its affects
- Binding site 4 proteins to increase rate of transcription
- -Do this by causing DNA btwn enhancer and promoter to loop out and interact w one another
- Position independent
72
Trp Operon
- Ex of neg repressible operon
- 5' UTR has 4 complementary regions
- --1 comp to 2
- --2 comp to 3
- --3 comp to 4
- ----Allows 5' UTR to make 2 secondary structures
73
Attenuation process of Trp Operon
- High levels of tryptophan--> no stalling of ribsome cuz tRNAs are charged
- --> Bping of 3 and 4, hairpin followed by Us--> attenuation
- Ribosome partially covers 2 when RNA pol finishes 3, so cannot BP
- --3 bps w 4 because it didn't w 2
74
Antiterminator process of Trp Operon
- Low levels of tryptophan--> stalling of ribosome cuz tRNA arent charged
- --> Bping of 2 and 3, hairpin not followed by Us--> No attenuation
- Ribosome stalls at trp codons UGG
- 2 and 3 bp because ribosome stuck at 1
75
Combinatorial Control
- Different combinations of activators and repressors determine transcription
- -Stimulates interaction of multiple regulatory proteins (activators and repressors) binding to enhancers and scilencers in diff combos
76
3 regions that euk regulatory proteins interact w
1. Core promoter
- -Upstream from gene regulating
2. Proximal elements
- -Found in reg. promoter, upstream of gene
3. Enhancers and Scilencers
- -Proximity-dependent, bind to activators or repressors
77
SWI/SNF complex
- Chromatin remodeling
- Uses energy from hydrolysis of ATP
- Slides or ejects nucleosomes, freeing promoters to bind to transcription factors and RNA pol 4 transcription
78
What does RNA pol do when it encounters nucleosomes? How does this differ for genes of diff transcription levels?
- Highly transcribed genes--> RNA pol ejects histones, nucleosomes reform on DNA behind RNA pol II
- Lowly transcribed genes--> H2A/H2B dimer is ejected, RNA pol moves around histone hexamer, nucleosomes reform behind RNA pol II
79
RNA interference
- A noncoding RNA targets complementary mRNAs w/in a cell for scilencing or degradation
1. miRNAs--> form small hairpins, mRNA unable to be translated
2. siRNAs--> degrades mRNA
80
Dicer
-Endonuclease that cuts the dsRNA into 21-25 bp fragments
81
RISC
- RNA-induced scilencing complex
- Degrades 1 strand of RNA
- Binds to target mRNA and..
- ---Cleaves and degrades
- ---Inhibits translation
- ---Attracts methylases and deacetylases, spreading heterochromatin
82
Wobble
- Occurs at 3rd position
| - Multiple mRNA codons can be recognized by the same tRNA
